Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
SV40T transformed fibroblasts
Sex
male
strain
129S1 X 129S1
cell type
SV40T transformed fibroblasts
antibody
None
cell type
IATRX Knock down (shATRX) Xist transgenic (X+P) cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were sonicated in a covaris S2, precleared with protein G agarose and protein-DNA complexes were precipitated using specific antibodies. Paired end ChIP-sequencing library preparation kit (E6240S) and Illumina multiplexing oligos (E7335S) were purchased from New England Biolabs. Libraries were quantified on a Bioanalyzer using the Agilent high sensitivity DNA kit (Agilent Technologies Cat. No. 5067-4627) and by qPCR using the KAPA library quantification kit (KAPA Biosystems Inc Cat. No. KK4824). Pooled samples were sequenced using Illumina HiSeq 2000 resulting in approximately 25-50 million of 50 bp paired-end reads per sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
27120000
Reads aligned (%)
97.6
Duplicates removed (%)
9.9
Number of peaks
203 (qval < 1E-05)

mm9

Number of total reads
27120000
Reads aligned (%)
97.4
Duplicates removed (%)
10.8
Number of peaks
195 (qval < 1E-05)

Base call quality data from DBCLS SRA